Sequence
atgc intronic sequence ATGC exonic sequence...ttttgctagcttttgttattgaattagattgccataattgcttaggttgctttcttttacttttgctacctccctttattgaagttttttgttgtcgcagGAGATATACTCAGTAAAATTACCTGGAAATCCCAAATTGGGAGAAGGGAAGCCCGAGAATCAAAATCATGCAATTATATTTACGCGTGGAAATGCAGTCC
Basic information
species | Glycine max |
transcript | GLYMA20G38860.1 |
intron # | 37 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 37
lower sequence: LOC_Os03g02756.1 (Oryza sativa), 3'ss of exon 1
-ttttgctagcttt-tgttattgaattagattgcc-ataattgcttaggttgctttcttttacttttgctacctccctttattgaagttttttgttgtcgcagGAGATATACTCAGTAAAATTACCTGGAAATCCCAAATTGGGAGAAGGGAAGCCCGAGAATCAAAATCATGCAATTATATTTACGCGTGGAAATGCAGTCC
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cccttgttaagtaaatatcatcagctaaagtagtttatatcatgtttggttatttgagtaacgtattaattcttctatgcaccaaataacttggctg---cagGAAATTTATTCCATTAAATTGCCTGGCAATTTTAAGCTGGGTGAGGGGAAGCCAGAAAACCAAAATCATGCCATAATATTCACCCGTGGAAATGCAGTGC
upper sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 37
lower sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 32
ttttgctagcttttgtt--attgaattagattgccataa-ttgcttaggt-tgctttcttttactt--ttgctacctccctttattgaagttttttgttgtcgcagGAGATATACTCAGTAAAATTACCTGGAAATCCCAAATTGGGAGAAGGGAAGCCCGAGAATCAAAATCATGCAATTATATTTACGCGTGGAAATGCAGTCC
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--ctggaggtctttgtttgaacactctaatttcaaataacttatctatctgtacttttatttatttatttgttatctcactgttatcagttatgttttt----cagGACATATACTCTATCAAATTACCAGGAAATCCTAAACTTGGTGAAGGAAAACCTGAAAATCAAAACCATGCAGTTATATTTACTCGTGGAAATGCAATTC
upper sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 37
lower sequence: PP1S88_136V6.1 (Physcomitrella patens), 3'ss of exon 33
ttttgctagctttt-gttattgaattagattgccataattgcttaggttgctttcttttacttttgctacctccctttattgaa-gttttttgttgtcgcagGAGATATACTCAGTAAAATTACCTGGAAATCCCAAATTGGGAGAAGGGAAGCCCGAGAATCAAAATCATGCAATTATATTTACGCGTGGAAATGCAGTCC
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tgttatcatctcgtagctactaaac--gaatggtattttacttctcactgctatcgagacaacaagctttaaagtgttaaggggtaaactattttaatgcagGAAGTATATTCCATTAAGCTCCCCGGAGACGTTAAGCTTGGTGAAGGAAAACCCGAGAATCAAAATCATGCAATAATTTTCACGCGTGGAGATTGCATCC
upper sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 37
lower sequence: EFJ07568 (Selaginella moellendorffii), 3'ss of exon 34
ttttgctagcttttgttattgaattagattgccataattgcttaggttgctttcttttacttttgctac-ctccctttattgaagttttttgttgtcgcagGAGATATACTCAGTAAAATTACCTGGAAATCCCAAATTGGGAGAAGGGAAGCCCGAGAATCAAAATCATGCAATTATATTTACGCGTGGAAATGCAGTCC
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--------------------------------------------------------gtacgctcgctatgcgttcaactttaatctaatcaggtactacagGATATCTACACTATCAAATTACCGGGAAATCCAAAACTTGGAGAAGGCAAGCCTGAAAATCAAAATCATGCGATTATTTTTACCCGTGGAGATGCAATAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgctttcttttacttttgctacctccctttattgaagttttttgttgtcgcagGAGATATACTCAGTAAAATTACCTGGAAATCCCAAATTGGGAGAAGGGAAGCCCGAGAATCAAAATCATGCAATTATATTTACGCGTGGAAATGCAGTCC
ttttttgtt CT-rich tract
tttattgaagtttttt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttgctagcttttgttattgaattagattgccataattgcttaggttgctttcttttacttttgctacctccctttattgaagttttttgttgtcgcagGAGATATACTCAGTAAAATTACCTGGAAATCCCAAATTGGGAGAAGGGAAGCCCGAGAATCAAAATCATGCAATTATATTTACGCGTGGAAATGCAGTCC
- - - - gcttttg
- - - - - - - - - - - - - - -tgccata
- - - - - - - - - - - - - - - - - - - tgcttag